Sunday, May 2, 2010

What’s the Alternative?

The most common question evolutionists ask, when presented with the many scientific problems with Charles Darwin’s theory, is “what’s your idea?” The simplest known form of life is immensely complex, if evolution is true then many advanced mechanisms of biology must have evolved early on—before they were needed, new species appear abruptly in the fossil record, adaptation occurs via intricate mechanisms that respond to the environment, similar species reveal profound differences, and different species reveal profound similarities. The fundamental predictions of evolution have gone wrong and so it would seem only natural to question the theory. Is it not reasonable for evolutionists to ask “what’s your idea?” It would seem so, but in fact that simple question reveals what is at the core of evolutionary thinking.

First, one must understand the sense of the question. What do evolutionists mean when they ask “what’s your idea?” What they do not mean is that they are having second thoughts about evolution. The false predictions and other empirical problems are not news to evolutionists. They know there are problems, but they are stored in a box labeled “Research Topics.” All you are doing is removing the items from the box and spreading them out on the floor. So what?

It is not that evolutionists are ignorant of these problems, or that they consider them to be irrelevant. Yes, there are some problems, but they just aren’t that important. Why? Because everyone knows creationism is false. As evolutionists explain, creation is both bad theology and bad science. If this were a multiple choice question, it would have a few choices that are obviously false, no question about it. The final choice makes sense and, in any case, must be the right answer because it is the only choice left.

This is the backdrop from which the question “what’s your idea?” is asked. It is not that evolutionists are following the evidence that leads away from evolution and want to know what direction to go. But on the other hand it is not that evolutionists are unwilling to consider alternatives. Indeed, at the core of evolutionary thought is the evaluation of alternatives.

In a Hegelian-like thesis / anti thesis relationship, evolution plays off of creation. Evolution needs creation’s foolishness. Without creation as the foil, evolution would be left with a box of scientific problems.

And what about these problems? Evolutionists rightly claim that most have been solved. But the solutions don’t make evolution any more likely. They merely shift the problem from a false prediction to a theory complication. One can always resolve a false prediction with a theory patch, but does that really solve the problem?

Evolutionists say that with science there is an inexorable march of progress as problems are continually resolved. In fact, with evolution, there is an inexorable march of just-so stories constructed to explain inconvenient facts.

But do inconvenient facts really matter if evolution is the only choice? At its core evolution is contrastive—it weighs the alternatives and makes the obvious choice. So when evolutionists ask “what’s your idea?,” they are revealing their core thinking. It is all about the failure of creationism. Evolution is a fact because it is the only possibility. But all of this hinges on a deep reservoir of metaphysics. Notions of uniformity, scientific method, what a good god would do, and the absence of unconceived alternatives all lurk beneath the surface. Religion drives science, and it matters.

143 comments:

Whatever you think of evolutionists, you have to admit that creationists simply don't have any answer to this question. Bill Dembski conceded as much when he wrote that "it's not ID's task to match your pathetic level of detail in telling mechanistic stories."

Dr Hunter is of course spot on, when evolutionists ask the question "what's your idea" they ask it with a rhetorical tone, what they mean by this is "surely you don't think all of this proves creation!, because that would just be ridiculous. I mean Darwin at least showed creation is false".

I applaud Dr Hunter for opening up his blog to criticism and for a relaxed moderation policy.

This place has become much more interesting (to me) than other ID sites, such as Uncommon Descent, thanks to Dr Hunter's focus on science and his willingness to let some very bright people have their say.

When evolutionists ask 'What's your alternative?' they are doing it to highlight the fact that there simply is no competing scientific theory.

I know I do.

Cornelius Hunter has just written a verbose article dancing around a profound problem he, Creationists and ID proponents have - they don't actually have a scientific theory or hypothesis to present as an alternative. ID and Creationism are not scientific theories. They are theological ideas. Not science.

And that is a very deep problem for Creationism/ID proponents. Because tear impotently as they like at the theory of evolution, it will continue to stand as long as no other theory accounts for more evidence.

As usual, Dr. Cornelius is greatly overstating the size and nature of alleged problems with evolutionary theory. He's short on details about the problems with evolution he alleges here, and when we point out that his scientific references frequently support evolutionary theory, he was silent, he evaded, he changed the subject.

In the thread immediately before this one, he alleged that one problem with evolution theory was that there were "major problems" (his phrase) in constructing phylogenetic trees from DNA because supposedly they don't match those constructed from fossils. Commenter RobertC took apart some of his other refs. I took apart the "major problems" ref that Cornelius cited. In that ref, DNA comparisons of whales and hippos shows that they are related by common descent.

Dr. Cornelius cited the paper, then he evaded the data in the paper he cited!

Now in this thread, we get more alleged major problems with evolution. What this time?

Cornelius: "if evolution is true then many advanced mechanisms of biology must have evolved early on..."

Early on? You mean three billion years after oceans and bacteria formed on earth?

Cornelius: "—before they were needed..."

Say what? What evidence is there for that? Totally bare assertion unsupported by facts.

"--new species appear abruptly in the fossil record"

But major vertebrate taxa do not. Take a look at Lindsay's list of diagrams of smooth appearance of species (non-technical.) Amphibians, as a taxa, did not. Mammals certainly did not. The pre-reptilian jaw bones morphed into the bones of the mammalian inner ear in a gradual process, every step nicely represented. The evolution of primates into humans, via Ardipithecus, Australopithecus into early Homo is gradual, especially where brain size is concerned. Australopithecus sediba is perfectly intermediate between A. afarensis and early Homo.

The specific mechanisms that Dr. Cornelius has cited in the past, do not contradict random mutation, frequently utilized increased rates of random mutation, and always involve a natural selection step. Natural selection is one form of response to the environment.

In this post, Dr. Cornelius now asserts that evolutionists won't change their theory because the alternative-- creationism-- is so horrifying.

Bull. Evolution theory has undergone two, two major modifications in response to new data. The first, of course, being the incorporation of Mendelian genetics in the so-called Neo-Darwinian synthesis.

The second being, the incorporation of horizontal gene transfer (HGT), which means Darwin's tree of life is no longer all tree, but is sometimes net-like. There's a ton of genetic data from genome projects, so much so that we have enough data to modify the tree into the occasional net-like pattern.

So, Cornelius's thesis is wrong: scientists do modify their theories, they are not so horrified by creationism that they won't modify their theory.

But pony up some data. And propose a theory in which the number of free parameters is smaller than the number of data points. This is true of HGT. But in creationism, the number of free parameters = number of data points. Science is and should be biased against non-predictive theories.

And all the chnages in the fossils in the nice diagrams, might be noirmal variation wihtin a species, or a physiological change.

And if there are from 1 to 10 million species that exist now, and from 20,000,000 to 1 billion species that are now extinct, I, for one, would expect to see a lot more examples of species to species change in the fossil record.

And since Tiktaalik is no linger considered an ancestor of the amphibians, the real ancestor is missing. Same thing with bords and archaeopteryx.

"Y'know,in the diagrams that where linked above, there is a daigram of one species of snail that shows a great deal of variation."

Yes, and the other diagram shows 330 separate species of plankton.

As for your question of how HGT works: there's more than one method. The most relevant for vertebrates is that a virus infects one animal-- virions have a high mutation rate, and insert their DNA into the host's genome-- and when the virion duplicates its DNA, a part of the host's genome breaks off and gets incorporated into the newly bred viral capsids.

Then that virus breeds and breeds, and infects another species. It inserts its DNA into the host cell. If it infects the gonads (egg cells or sperm-producing), the viral DNA from the other organism can get stuck in the new animal produced from the infected egg or sperm.

These viral insertions in the genome can be recognized because they are often flanked on either side by viral DNA sequences. As I said before, HGT makes evolution theories more complex, but we have more data to fit against a more complex theory, thanks to the genome projects.

A very important protein involved in the formation of the human placenta is of viral origin, co-opted to assist in facilitating nutrient transfer through the placenta from mother to offspring. Think about that. The effects of an ancient viral infection made humans human.

'Because everyone knows creationism is false. As evolutionists explain, creation is both bad theology and bad science.' - this is a fundamentally correct statement. As I have said before, every time a scientific paradigm, principal or theory is found to be lacking or inaccurate it is replaced by stronger scientific knowledge or proof, never by the possibilty of an agency such as a creator. The evidence mounts inexorably.Many of the contradictions stated in the opeing paragraph are false. To attempt to extrapolate the relatively small number of gaps and anomolies as justification for doubt are tenuous at best. The weight of evidence is still insurmountable.'It is all about the failure of creationism' - another true statement. 'But all of this hinges on a deep reservoir of metaphysics. Notions of uniformity, scientific method, what a good god would do, and the absence of unconceived alternatives all lurk beneath the surface.' - pro-creationist mumbo-jumbo.'Religion drives science, and it matters.' - you keep stating this shibboleth. Are you not aware of the definition of insanity? If you kkep repeating the same behaviour......

Actually that is not true (I assume you are referring to empirical evidence). In fact the evidence is all over the map. There is substantial evidence for evolution, but there are also substantial problems. Most of the problems are handled with theory complications, or just not handled. Statements such as "there is no evidence for evolution" on the one side, or "the evidence is insurmountable" on the other, are simply non scientific hyperbole. The actual state of the evidence, as it bears on evolution, is far more complex. There are many ways to evaluate the evidence, many metrics are possible, and so forth, but the "evolution is a fact" conclusion comes from metaphysical premises, not merely from the empirical evidence.

What is the purpose of your posts?Certainly not to promote the study, education or advancement of the science of the theory of evolution (and don't give me your crass 'it's only a theory' nonsense - see, germ theory), or even science in general.

Your purpose is to submit articles based on any little topic you think you can use to raise doubts about evolution in an attempt to devalue it. Such as rapid adaption bringing evolution into question. Yes there are gaps, yes new information comes to light and yes new discoveries raise question marks over the current thinking. But at the risk of repeating myself ad nauseum 'every time a scientific paradigm, principal or theory is found to be lacking or inaccurate it is replaced by stronger scientific knowledge or proof, never by the possibilty of an agency such as a creator'.

I have not yet seen you clearly enunciate any scientifically evidential alternative. You merely attempt to poke holes in the science of evolution without suggesting what may be the 'truth'.

But we all know the 'truth' don't we. Your only purpose is to perpetuate the myth of creationism/ID with your futile attempts to call evolution into question. So what value do you add other than preaching to the converted?

If you insist on posting articles which claim to evidence the flaws in evolution, when will you start stating which theory those flaws don't disparage? If it's not evolution, what is it?

Religion drives twisted, perverted and misrepresented science, and that really does matter!

What is the purpose of your posts?Certainly not to promote the study, education or advancement of ...or even science in general.===

That is one of the purposes, as I have stated here in the past. People need to understand evolution, but I also hope to spur interest in science.

===But at the risk of repeating myself ad nauseum 'every time a scientific paradigm, principal or theory is found to be lacking or inaccurate it is replaced by stronger scientific knowledge or proof, never by the possibilty of an agency such as a creator'.===

Point being?

===I have not yet seen you clearly enunciate any scientifically evidential alternative. You merely attempt to poke holes in the science of evolution without suggesting what may be the 'truth'.===

Is there not value in understanding the religion that evolutionary thought inserts into science?

===But we all know the 'truth' don't we. Your only purpose is to perpetuate the myth of creationism/ID with your futile attempts to call evolution into question. ===

Where did I say that?

===If you insist on posting articles which claim to evidence the flaws in evolution, when will you start stating which theory those flaws don't disparage?===

I doubt anytime soon since I am not in possession of any such theory. But in any case, so long as religious mandates are driving science to absurdities, presenting any alternative explanation would be a waste of time. The first step for the alcoholic is to understand there is a problem.

===Religion drives twisted, perverted and misrepresented science, and that really does matter! ===

===But we all know the 'truth' don't we. Your only purpose is to perpetuate the myth of creationism/ID with your futile attempts to call evolution into question. So what value do you add other than preaching to the converted?===

You're projecting. It is you, not I, who is the religious person here.

There is substantial evidence for evolution, but there are also substantial problems.

As long as there is any evidence for evolution at all, it will stand until another theory comes along which explains more.

'What's your alternative?' is not an unreasonable question for evolutionists to ask. It is a perfectly sensible one. Because unless someone comes up with one, biology will continue to be built around the theory of evolution.

Your apparent afront at this very question being asked (without actually answering it, I should point out) betrays your unease with it. But it remains a perfectly valid one, and your failure to simply address it speaks volumes.

Point out what you see as flaws in the theory of evolution if you like. Many scientists do this routinely - except they phrase their quibbles as questions and actually do some research and try to solve the issues that irk them. But if you want the theory of evolution as a whole to just go away, that is simply not going to happen while it remains by far and away the best-evidenced theory which accounts for natural history and diversity.

'Point being?' - you call evolutionary science into question on the flimsiest of pretexts with the motive of promoting creation/ID yet there is no evidence for creation/ID. Insurmountable evidence, that's the point.

'Is there not value in understanding the religion that evolutionary thought inserts into science?' - say what? Evolutionary thought does not possess any religion to insert. That's the purpose of your articles predicated on creation/ID.

'Where did I say that?' - um, with every post calling evolution into question and trying to align evolutionary science with religion. Oh, and did you not notice where your blog is placed? Or the convictions of those who strive valiantly to support you? We don't all need to be hit in the face with a bat to get the point or the meaning, we leave that to fundies.

'I doubt anytime soon since I am not in possession of any such theory' - I question the veracity of your claim, see every reason stated above. '...so long as religious mandates are driving science to absurdities, presenting any alternative explanation would be a waste of time' - yet your religious mandates are driving your science to absurdities. You do present your alternative, just not in a clear and open manner.

'The first step for the alcoholic is to understand there is a problem' - I wish every person of 'faith' could understand and accept this. Faith is a crutch the same as excessive use of alcohol is.

'Agreed.' - yeah, but you see, the problem is, I'm on the side of reality not fairytales.

Again, you seem to have things backwards. Evolution entails strong religious / metaphysical beliefs and evolutionists seem to have difficulty understanding empirically-based conclusions. They always seem to impute religious motives while, hypocritically, they are the ones who have such motives.

'Belief in god does not mandate a position on evolution. Theists are all over the map on this.' to an extent, but the basic rationale of abrahamic religion is of god the creator. Some choose to believe in god but accept evolution. How they manage to do so is up to them.

'It is the atheists who have no choice when it comes to evolution.' - well we do actually. Some believe in the white mice theory, some in the Erich von Danekin theory and others in a few other equally preposterous ideas. Sound familiar, that's right, the 'creator' principle. But the sane, rational and evidential ones accept evolution.

You however, choose to promote creation/ID, to claim not to do so on religious grounds is disingenuous. If I am wrong, when are you going to enlighten us with your alternative theory to evolution with supporting evidence?

Um, there is no empirical evidence for creation/ID. Again, if I am wrong, please feel free to clearly prescribe such.

'Evolution entails strong religious / metaphysical beliefs and evolutionists seem to have difficulty understanding empirically-based conclusions. They always seem to impute religious motives while, hypocritically, they are the ones who have such motives.' - You consistently state this nonsense which is a complete inversion of reality. Can I refer you to the theory of insanity again?

I have delayed responding as I found we were almost 'talking' over each other just above and that doesn't help anyone.

You continue to refrain from responding to my questions regarding your alternative theory to evolution and any scientific evidence you may have for it.

You continue to deny that creation/ID is religious based. How you can do so is indicative of the denial of reality which drives most of your extrapolated arguments.

You continue to claim that evolution is driven by religion. Well guess what, I'm going to agree with you! Evolutionary science can be driven by religion to the extent that the fantasies proposed by creation/ID need to be refuted by scientific evidence.

Any other statements you make lack any truth or evidence and appear to simply be a case of sticking your fingers in your ears and going 'La La La'. Theory, evidence for - come on, where is it?

No, I explained I don't have one. This is typical of discussions with evolutionists. You answer a question, and it keeps on coming back, apparently because the evolutionist can't think beyond his own assumptions.

"You continue to deny that creation/ID is religious based."

Again, no, I said *I* don't have a religious dog in the fight. I could care less if evolution is true or not.

The fact that evolution is based on religious or claims is hardly a heroic claim. Metaphysics runs all through the literature, and every proof for evolution entails the metaphysics. And evolution's use of metaphysics has been described in the peer-reviewed literature (described by an evolutionist and peer-reviewed by evolutionists).

===Define this 'religion that evolutionary thought inserts into science' of which you speak for me then. Clearly and unequivocally. Maybe I'm missing something.===

I'll skip antiquity and use modern science as our starting point. Beginning in about the mid 17th c., Christians began some "new" traditions regarding their explanation of divine creation. Nicolas Malebranche (Roman Catholic), Thomas Burnet (Anglican) and Gottfried Leibniz (Lutheran) are representative thinkers, but there are many more. They argued strongly that god would/did exclusively use natural laws to create the world.

===Define this 'religion that evolutionary thought inserts into science' of which you speak for me then. Clearly and unequivocally. Maybe I'm missing something.===

This continued and proliferated in the 18th c., with several traditions arguing for a naturalistic origins for several different religious reasons. By the time Darwin came along these traditions had become fairly strong, with many religious and secular voices calling for naturalistic origins (including no less than the lord chancellor of England when Darwin was a teenager).

===Define this 'religion that evolutionary thought inserts into science' of which you speak for me then. Clearly and unequivocally. Maybe I'm missing something.===

The metaphysical push for naturalistic origins could be seen in pre *Origins* works, such as *Vestiges* (Robert Chambers). And Darwin and Wallace constructed the more sophisticated theory of evolution based on the same motivations. Darwin's book is full of religious claims he didn't need to defend. They were a given by 1859. See, for example:

===Define this 'religion that evolutionary thought inserts into science' of which you speak for me then. Clearly and unequivocally. Maybe I'm missing something.===

So the evidences and arguments for evolution, and claim that it is a fact, are based on deep metaphysics, while the actual explanation has produced a steady stream of false predictions.

And the metaphysics that evolution entails is no less the case today. You see it when evolutionists argue for the theory (as opposed to merely investigating, and presupposing, the theory). See this, for example:

===Define this 'religion that evolutionary thought inserts into science' of which you speak for me then. Clearly and unequivocally. Maybe I'm missing something.===

So to summarize, the result of religious thought driving science is an origins story that is silly beyond measure. The idea that all life, from the hummingbird to plankton, and all the mechanisms, from the DNA code to the carbon cycle, just happened to arise from the blind play of the laws of thermodynamics, electromagnetism, the laws of motion, and so forth, is the greatest joke religion has ever played.

But that's not anywhere near the end of it. For perhaps there are things we don't understand about nature. Perhaps evolution did occur. That certainly is possible. But evolution doesn't stop there. They claim evolution is a scientific fact every bit as much as is gravity. Now that is false, and so obviously false it is incredible that it is so widespread.

Folks can certainly argue evolution is true, or a fact. There are plenty of powerful metaphysical arguments for evolution. But this is not science.

is that it? You think you can leap from 150 years ago to now and pretend it's all premised, evidenced and investigated on the same basis?

In that time period there have been hugely significant and rapidly accelerating advances in all disciplines of science.

The discoveries and advances made, between for example 1400 and 1600, are absolutely miniscule compared to that made in even a decade now.

The names you list are people who were intelligent enough to realise that god and creation/ID was an inadequate explanation. They were able to initiate investigations which took place on a non-threatening level so weren't subject to the usual acrimony.

There may have been an element of metaphysics to their actions in that era but that certainly isn't the case today.

Your previous posts which you cite add no weight to your case as they are all driven by the same underlying cause and espouse the same principles.

To claim that religion drives evolutionary science today, other than the example I gave earlier, is a banal statement no different to 'god said it, I believe it, that settles it'.

"You think you can leap from 150 years ago to now and pretend it's all premised, evidenced and investigated on the same basis?"

There is no such leap. The 20th c. was no different. Evolutionists throughout continued with the same logic. I have a chapter of representative mid 20th works in my book *Darwin's God*, and then later works in other chapters, and my other books.

"In that time period there have been hugely significant and rapidly accelerating advances in all disciplines of science."

Yes, indeed. And the false predictions came faster and faster.

"The names you list are people who were intelligent enough to realise that god and creation/ID was an inadequate explanation. They were able to initiate investigations which took place on a non-threatening level so weren't subject to the usual acrimony."

No, be careful. Evolutionary thought is based on its own metaphysics. Here's a simple example, but there are many more: evolutionists argue strongly that the nested hierarchy disproves creation or design, and therefore we must have evolution, somehow. But no creationist (or scripture) ever said god would not create in such a pattern. Evolutionary thought arises from particular traditions within Christian thought. Evolution is a Christian theory of origins, in the sense that it comes from particular traditions with Christian thought.

"There may have been an element of metaphysics to their actions in that era but that certainly isn't the case today."

"Here's a simple example, but there are many more: evolutionists argue strongly that the nested hierarchy disproves creation or design, and therefore we must have evolution, somehow."

And let me add to what I said. Why is it that the nested hierarchy, and many other examples, is taken as such powerful evidence for evolution? After all, it would do no harm to evolution if there were no such pattern. Evolution can appeal to multiple OOL events, or to temporarily rapid spurts of evolution, either of which would mean we would see no such pattern. Furthermore, even if you did have a hard and fast prediction which was fulfilled, all it would be is a successful prediction. That's not a real big deal. But as was finally pointed out in a peer-reviewed paper, the reason why such observations are taken to be so powerful is because they rebuke creation. It's the low probability of creation that such observations imply, that makes them so powerful. But that inferred low probability is, itself, a deeply metaphysical claim. And it comes right out of Kant, Burnet and other Enlightenment thinkers. This isn't about science.

'in the sense that it comes from particular traditions with Christian thought' - yep, the ones which were considered blasphemous if evolutionary statements were said too loud. And then they drifter further and further from religion.

'Of course it is. It is rampant today.' - strongly disagree, too many scientists focussed on minutely detailed aspects of science too busy to have metaphysical thoughts about why. They observe, test and reveal facts and evidence. Do not equate comparison or extrapolation as a suggested starting point for investigating something with metaphysics.

http://darwins-god.blogspot.com/2010/02/jerry-coyne-why-embryology-proves.htmlhttp://darwins-god.blogspot.com/2010/02/coyne-evolutionary-arguments-not.html using your own opinion as evidence for your opinion, what do they call that?

//Define this 'religion that evolutionary thought inserts into science' of which you speak for me then. Clearly and unequivocally. Maybe I'm missing something.//

Of course you are missing something, all evolutionists miss this, otherwise you wouldn't say things like "God wouldn't do x" or "God wouldn't create cats to play with mice". Evolutionists don't understand why statements such as these are theological, they don't understand that arguments of this nature cannot be used in support for evolution, otherwise you would never say it in the first place.

The names you list are people who were intelligent enough to realise that god and creation/ID was an inadequate explanation.//

This is the problem, it was inadequate for religious and metaphysical reasons. As Darwin himself said 'God wouldn't create cats to play with mice'---ie therefore we know at least one way or another evolution has to be true.

So to summarize. You post article after article with one purpose in mind. An attempt to discredit, disparage and devalue evolutionary theory. This is because you are a creationist/IDer.

You claim to not be offering an alternative to evolution yet all the evidence says otherwise.You repeatedly assert that evolutionary theory is driven by religion. This is in an attempt to falsely create a level playing field on which to compare evolution with creation/ID with some level of equivalence despite the insurmountable evidence for evolution.

You keep claiming metaphysics in regard to evolution in an effort to make science appear less scientific and more ethereal.

A little tip for you. If someone tried to convince me that two plus two equals five, I would call them out on it even if they happened to be the most brilliant and world renowned mathematician.

All this and more is perpetrated by one Cornelius Hunter whose attached profile appears under the heading of the Discovery Institute. Cornelius tells us he is adjunct professor at ‘a private Christian university ‘….. where all faculty, staff and students are professing Christians….. committed to biblically centered education, intentional spiritual development and vocational preparation’. A place where in the School of Arts & Sciences students in the school of biological science will learn ‘…the integration of biological facts with spiritual principles…’ and will demonstrate ‘An ability to discuss theories of origins and evolution within the context of a Scriptural view of creation’ and whose doctrinal statement includes ‘The Scriptures of the Old and New Testaments are without error or misstatement in their moral and spiritual teaching and record of historical facts. They are without error or defect of any kind‘ and ‘Man was created in the image of God,’

johan - otherwise you wouldn't say things like "God wouldn't do x" or "God wouldn't create cats to play with mice" 'otherwise you would never say it in the first place.'- I don't, and not many evolutionists do.'This is the problem, it was inadequate for religious and metaphysical reasons' the important word being 'was'. Evolutionary theory and the applied science have moved well beyond this ancient paradigm.

Evolutionary theory and the applied science have moved well beyond this ancient paradigm.//

a) evolutionists today like Jerry Coyne, etc still defend Darwin (who argued and was convinced evolution was true for religious and metaphysical reasons). Was Darwin just lucky? Used these theological arguments and then it turned out he never needed them? I doubt

b) Darwinism which started with Darwin still forms the core of evolutionary theory today, meaning if there is something suspicious about Darwin's reasons and arguments about why evolution was true, this means there is reason to believe there is something suspicious about evolution today.

I can recognize evidence for design in nature because unlike Darwin, I don't feel theologically or religiously obliged to rule out design. I understand why theological arguments are irrelevant as far as the scientific question of design is concerned. It's for this reason that I am less impressed with Darwin's mechanism and interpretations of the evidence.

johan, Darwin may have needed them at the time. Think about where he started from and the social/religious mores of the time.

'if there is something suspicious about Darwin's reasons and arguments about why evolution was true, this means there is reason to believe there is something suspicious about evolution today' what rubbish. Look at the scientific evidence and proof which exists now and is growing exponentially. Your statement is fatuous. That's like saying 'I used to be suspicious about claims that the earth is flat, now I'm suspicious about claims that the earth is round.'

'I can recognize evidence for design in nature because unlike Darwin, I don't feel theologically or religiously obliged to rule out design.' = you're kidding right? So what are you, a white micer or an Erich von Danikener? You're still a creationist/IDer.

People like Darwin wasn't bothered by evidence of design in nature, he couldn't care less if he was staring this evidence in the face, that is because Darwin for religious and metaphysical reasons "knew" evolution had to be true. Take away this theological obligation and you can easily recognize the evidence for design itself.

It's absolutely crucial to presuppose the necessary metaphysical presuppositions before one can come to the deduction that evolution is true. Like I said, Darwin must have been very lucky indeed if it turned it he never needed to rule out design for theological reasons because there happen to be no evidence for design anyways. If Darwin was a gambler he wouldn't be allowed in casinos.

That's like saying 'I used to be suspicious about claims that the earth is flat, now I'm suspicious about claims that the earth is round.//

Evolution today still has Darwin's theory at it's core: blind material processes did the job one way or another.This is Darwin's pathetic legacy and this still forms the core of evolution today.Darwin believed he was obliged to blame complexity on blind material processes not because he had any evidence for this, but because he knew for metaphysical reasons the alternative was false. The nature of the evidence is as irrelevant today as it was in Darwin's time, because of the religious assurance that evolution has to be true.

Cornelius wrote: Here's a simple example, but there are many more: evolutionists argue strongly that the nested hierarchy disproves creation or design, and therefore we must have evolution, somehow. But no creationist (or scripture) ever said god would not create in such a pattern.

That's a bizarre claim. Theory of evolution does not win because creationism fails. It wins or loses on its own merits. Creationists don't make any testable predictions. (How could they? God is not bound by any considerations.) A nested hierarchy of clades is a positive prediction of evolutionary theory.

Evolutionary thought arises from particular traditions within Christian thought. Evolution is a Christian theory of origins, in the sense that it comes from particular traditions with Christian thought.

That's pretty vague. Do you mean to say that scientists who advanced theory of evolution were Christians, therefore theory of evolution has Christian roots? That would be silly as it would also make electrodynamics a Christian theory of electricity. Perhaps you should expound on that.

Why is it that the nested hierarchy, and many other examples, is taken as such powerful evidence for evolution? After all, it would do no harm to evolution if there were no such pattern.

If there were no evidence for descent with modification, any conceivable theory of “evolution” would be markedly different from the current theory. The harm to the current theory would be its complete destruction, if you want to call that “harm.”

"In the final analysis the hierarchic pattern is nothing like the straightforward witness for organic evolution that is commonly assumed. There are facets of the hierarchy which do not flow naturally from any sort of random undirected evolutionary process. If the hierarchy suggests any model of nature it is typology[4] and not evolution. How much easier it would be to argue the case for evolution if all nature’s divisions were blurred and indistinct, if the systema naturalae was largely made up of overlapping classes indicative of sequence and continuity." --Michael Denton-- honest evolutionist 1986, 136-137

I can recognize evidence for design in nature because unlike Darwin, I don't feel theologically or religiously obliged to rule out design.

Scientists rule out design because it is not scientific. The restriction they place on themselves is to deal in theories supported by evidence. And yes, that does rule out design.

If design was presented as a hypothesis - with detailed, testable predictions and carefully laid out perameters on what would and what would not disprove it, then yes, it might be science. But it is not.

Saying 'I don't feel theologically or religiously obliged to rule out design' is like saying 'I don't feel theologically or religiously obliged to rule out demonic possession as an explanation for illness'.

And of course, let's not let this one from Cornelius slip by without comment:

(on alternative theories) No, I explained I don't have one.

Well bravo for admitting what we already knew. But again, this is why your criticisms on evolution - however valid (and I'm being extremely generous here because it seems to me the vast majority are as not nearly as valid as you seem to think) are rather futile. The theory of evolution, like every theory in science, will stand until it is surpassed by a better one.

The reasons evolutionists argue hierarchic pattern is evidence for evolution is for religious reasons---God wouldn't do it like this. Also the evidence for evolution evolves all the time, at the time when it was believed that embryos resemble on another during early stages of development this too was evidence for evolution. Just as was non-protein coding regions of dna. Whatever we think happens to be the case, that evolutionists try and sell as evidence for evolution. Evolutionists today argue that dissimilarity among embryos during early stages of development is actually evidence for evolution, again only because we know today that embryos are vastly dissimilar during early stages of development. The job of the evolutionist is to sell evolution, whatever the evidence is, that somehow has to be evidence for evolution.

“I own that I cannot see as plainly as others do, and as I should wish to do, evidence of design... There seems to me too much misery in the world... beneficent and omnipotent God would have designedly created the [parasitic wasp] with the express intention of their feeding within the living bodies of caterpillars, or the cat should play with mice.” –Charles Darwin, 1860

There is or there cannot be evidence for design in the natural world in the mind of Darwin, because God would not have created cats to play with mice. Darwin felt theologically obliged to blame complexity on blind material processes. What Darwin didn't understand was that theological objections however interesting they may be are actually quite irrelevant as far as the scientific question of design is concerned. If we were created by an evil or cruel God, and you could prove this God was cruel or evil, this doesn't mean we now evolved, meaning we were not created. The explanation for a sculpture doesn't change if you could somehow prove a sculptor was cruel or evil, following evo-logic would lead us to search for the explanation in the rock if we could somehow conclude the sculptor was evil.

David, I fully agree with Dr Hunter and Michael Denton on this one, it would have been easier to argue for evolution if there was no pattern. Also based on the evidence from embryology, junk DNA, it's fair to say that if we knew today that there was no pattern, evolutionists would have argued this is evidence for evolution. [and it would have been better evidence too if this was actually the case]

The quote you cited from Darwin is an example of an argument against Creationism, fair enough. But you make the same mistake as Cornelius in erroneously believing the theory of evolution is BASED UPON such arguments against creationism. It is not. It is built upon the large pile of evidence supporting it.

Evolution is not based on any assumption on what a divine creator would or would not make.

Such ponderings on what a divine creator would or would not make PRESUPPOSE the existence of such a being in the first place. And there is not the slightest evidence for one. So using one to explain natural observations is profoundly unscientific.

Also, I know you were addressing David, but I couldn't let this one go by without comment:

"...at the time it was believed that embryos resemble one another at early stages of development."

They do. And this is very compelling evidence for the theory evolution.

//What kind of "easier to argue for evolution" do you and Drs Hunter and Denton envision?//

David, In the words of Denton, that "nature’s divisions were blurred and indistinct, if the systema naturalae was largely made up of overlapping classes indicative of sequence and continuity". If evolution was so inevitable and if life will inevitably evolve, surely life evolving multiple times from non-living matter would make the case so much more powerful for evolution. And there is no reason why there should be any relationship between these different ancestors that evolved from non-living matter. There is no reason why anything should evolve in parallel if random mutations brought on the changes that lead to more complex life forms.

The quote you cited from Darwin is an example of an argument against Creationism//

Richie, not at all, this is actually Darwin's argument against design in nature, design in nature is not the same as creationism.

//erroneously believing the theory of evolution is BASED UPON such argument//

Thanks to Charles Darwin, we are now suppose to believe that evolution is blind and unintelligent. So it's crucial that we go back to Darwin to try and understand why Darwin believed evolution was blind and non-teleological.

//Evolution is not based on any assumption on what a divine creator would or would not make.//

Origin of species are full of these straw god arguments, for example animals migrating to different oceanic islands was actually claimed to be evidence for evolution Darwin argued because his straw god would have created the animals independently on the different islands. All Darwin had to prove was that some animals migrated to oceanic islands.

//PRESUPPOSE the existence of such a being in the first place//

Oh Darwin believed in God all right, just that he thought God would be in a lot of trouble if God was directly involved in Creation. Darwin felt evolution could get God off the hook, this is why many theologians were excited about his idea while the scientists were less impressed.

//They do. And this is very compelling evidence for the theory evolution.//

Jerry Coyne argues that the dissimilarity of early vertebrate embryos can be explained in the light of Darwin’s theory, since “the earliest stages of vertebrate embryos show adaptation” to the conditions of their existence. Funny when evolutionists thought the opposite was some of the most powerful evidence for evolution.Evolutionists such as Coyne have no shame in regarding this as evidence for the theory, Coyne writes: “Wells repeatedly fails to grasp the evidential value of phenomena [i.e., dissimilarities in early embryos] that can be understood only as the result of a historical process.”

I was thinking the other day, if science were not religious, it would have to allow for at least the possibility of the supernatural. But if science doesn't allow that possibility, it becomes religious, because it has formed a religious opinion.

The fundamental hypocrisy in Dr. Cornelius' argument is that he supports creationism/ID (comment above, May 2, 2010 8:57 PM), so he thinks creationism is a scientific hypothesis. However, when Darwin points out the serious flaws in all creationist hypotheses, then Cornelius says he's using a religious, theological argument. Bull. Cornelius himself defines creationism as scientific (and it was defined as a scientific hypothesis in Darwin's era) so Darwin's arguments against creationism are scientific arguments by Cornelius' own defintion of science, no matter whether Darwin's arguments sound like theology or not. By Cornelius' own defintion of science, which includes creationism, an argument (like Darwin's re: ichneumon wasp, above) can be both scientific and religious at the same time, because Cornelius and scientists of the 19th. century considered creationism as a scientific hypothesis. Because you define creationism as a scientific hypothesis, you have no grounds on which to bitch when Darwin points out the insurmountable flaws in your hypotheses. You have no grounds to dismiss this as theology, because you, Dr. Cornelius and Johan, you, not Dawkins, not PZ Myers, you define creationism as a scientific hypothesis, therefore Darwin's refutation of it is a scientific argument by the definition of science that you are pushing.

The hypocrisy is that you want to have your cake and eat it too. You want to define creationism as 'scientific', but then when your competitors point out the flaws in all your variants of creationism, then you whine that he's being religious! Bull! You just defined creationism as being a scientific hypothesis!

If creationism is a scientific hypothesis, as you indignantly insist, and as was the case in the 19th. century, then Darwin is right to use the ichneumon wasp argument, to consider the scientific merits of your hypothesis!

In short: if your Intelligent Designer is all-loving, then parasitism, predation, disease, aging etc. reject this variant of creationism.

If your Intelligent Designer is loving some times, hostile other times, indifferent other times, and *there are no independent observables* by which you can predict his "MOOD", then your theory can accomodate all data. Thus predicting nothing!

And that GOES DOUBLE FOR YOUR OBJECTIONS REGARDING NESTED HIERARCHY!

If your Intelligent Designer is constrained by nested hierarchy, it's no better than evolution-- and it's disproven by horizontal gene transfer! Ha ha!

If your Intelligent Designer is not constrained by nested hieararchy, it can accomodate all data, thereby predicting nothing!

You hypocrites want to be called scientists, and you want your creationism to be defined as science, so OK, Darwin treats it like that and you lose-- by the standards of science! But don't call his rejection of your inferior hypothesis "religious"!

You demand to play basketball, then bitch when the other guy dunks in your hoop!

Let me begin by making the following assertion: Everything either is or is not a simulation. Examples of simulations include complex computer programs, novels, and dreams.

My alternative to evolution, and scientific naturalism in general, is simply that all, or nearly all, of the known universe is a simulation, most likely in some kind of computer.

This hypothesis explains where materialist fantasies that were invented to justify materialism, like dark matter, fail.

Any area in which known forces are at a loss is in fact the result of malfunction, a software virus, or a deliberate program modification (or whatever is analogous in the simulation to those things in ours). Apart from such exceptions, nature proceeds as guided by the master software. This much is obvious, and was realized (in another form) by Plato, among countless others.

It's empirically testable, because we are very much capable of using scientific and mathematical tools to identify anomalous (hence simulation-aberrant) phenomena all the time. We've even begun work on developing tools to positively predict what sort of aberrations will next be encountered, based both on what we know of the nature of simulations and what we have learned so far about this one. (This last area still needs some work, I admit.)

Meanwhile, cosmologists are free to disprove us any time simply by producing, for example (just a few of many possibilities), a black hole, a star, or dark matter in a lab environment.

Do you deny that computers exist? Do you deny that computer simulations exist? Do you deny the relevance of computing to sciences such as astronomy and biology?

If you wish to argue that my hypothesis as given is unscientific, you are, without any warrant, ruling out an entirely possible state of affairs.

Cornelius: "Not real clear. Is "god wouldn't use a nested hierarchy, so evolution must be the cause" not religious?"

You support creationism and define creationism as a scientific hypothesis. Therefore, any attempt to narrow down the many, many free parameters in your preferred model is a scientific counter-argument, and possibly religious also, because you, Cornelius, define "God can do anything he wants" as a scientific hypothesis.

Therefore Darwin's quote about the ichneumon wasp is both religious and a fair scientific objection, by your, your, your, your defintion of science, which includes your hypothesis "God can do anything he wants."

If your Intelligent Designer is constrained by nested hierarchy, it's no better than evolution-- and it's disproven by horizontal gene transfer!

If your Intelligent Designer is not constrained by nested hieararchy, it can accomodate all data, thereby predicting nothing! And theories which predict nothing lose in scientific competition.

You hypocrites want to be called scientists, and you want your creationism to be defined as science-- so OK, Darwin treats it like that and you lose-- by the standards of science! But don't call his scientific rejection of your non-predictive hypothesis "just religious"!

"Is "god wouldn't use a nested hierarchy, so evolution must be the cause" not religious?"

using a random distribution (i.e. not a nested hierarchy) as a null model is a standard in all hypothesis-based statistical tests. or else you would say that the results of all statistical tests are religious, e.g.

"God wouldn't make the results of this drug trial different than random at the level of p<0.05 , so the drug must be the cause of these people getting better."

Cornelius,I'm saying that that is not the argument they are making, unless you think all statistics are religious. They are making a standard statistical argument, testing a hypothesis against a null hypothesis. You can open up any journal in any scientific field and see it being done. Do you think that all hypothesis-based statistics are religious?

Darwin's ichneumon wasp quote is a SCIENTIFIC argument, and arguments about Nested Hierarchy are SCIENTIFIC arguments, by Dr. Cornelius's own definition of science. Dr. Cornelius defines creationism/ID and "God can do whatever he wants" as scientific hypotheses, within the realm of science, therefore any author who refutes Cornelius' hypotheses-- because they can accomodate any data set, thus predicting nothing, thus being scientifically useless-- is using a scientific argument, according to Dr. Cornelius' own personal defintion of science, which includes creationism and "God can do whatever he wants" as scientific hypotheses.

So Darwin or you or me shooting down his hypotheses are scientific rebuttals, by Cornelius' own definition of science.

"No, they are not, unless you consider all frequentist statistics to be religious. do you think that all statistics are religious?"

Of course they are when the hypothesis is metaphysical. Here's an example I'm going to blog about. A creationist considers the nested hierarchy. He gathers data, models the data, performs a standard statistical argument, testing a hypothesis against a null hypothesis. The null hypothesis is strongly rejected (10^-200) and he concludes that creationism is therefore a fact.

He shows the analysis to the evolutionist who says "wait a minute, your analysis entails metaphysical assumptions." the creationist denies any such thing, explaining as he walks out the door that you can open up any journal in any scientific field and see null hypothesis testing being done. "Do you think," he asks, "that all hypothesis-based statistics are religious?"

I hope it is clear that you are the creationist. Evolution is a religious / metaphysical theory.

Well, OK. But if so, so what?(1) Does it invalidate the theory?(2) Is there another theory--any other, in biology or elsewhere--that is NOT a religious/metaphysical theory?(3) Can you explain how to consider the nested hierarchy properly?

Well, OK. But if so, so what?(1) Does it invalidate the theory?============

No.

=====(2) Is there another theory--any other, in biology or elsewhere--that is NOT a religious/metaphysical theory?=====

I define a theory to be "religious/ metaphysical" if it has religious/ metaphysical *premises*. If you say "god wouldn't do it that way" in your premises, as evolutionists do, then I think it is metaphysical.

OTH, if you *conclude* that the evidence suggests that natural law, as we understand it, is insufficient, and therefore the evidence supports creation, then I think it is not metaphysical.

I justify these definition as follows. In the former, a metaphysical premise is a given, you can't argue with it. Science cannot say anything about it. As philosophers say, the metaphysics is what happens *before* the physics (science) happens.

But if you *conclude* for a non natural cause, then there is a syllogism that can be evaluated. You have evidence, logic, and a conclusion. The conclusion can be rejected if the evidence is flimsy, logic fallacious, etc.

But evolutionists define it in exactly the reverse. They think metaphysical premises can be made all day long without the theory becoming metaphysical, but conclusions must be strictly naturalistic, or else it is metaphysical.

Which definition do you agree with, or do you have another?

======(3) Can you explain how to consider the nested hierarchy properly? ======

Long story, future blog, but I don't have any zingers. I'm not that smart.

Cornelius,If the creationist did this, I would ask him why the nested hierarchy is a specific prediction of creationism. It is a specific prediction of evolution because, if common descent is correct, the current state of the descendent should be dependent only on the changes that have occurred since the split from the last common ancestor. THis pattern is described by Markov chain processes, which produce nested hierarchies. THus, we are testing the hypothesis that patterns of descent fit Markov chain models against the null hypothesis that they do not. What is the creationists' justification for his prediction of the same thing?

===It is a specific prediction of evolution because, if common descent is correct, the current state of the descendent should be dependent only on the changes that have occurred since the split from the last common ancestor.=====

False, evolution does not predict that pattern to be observed, for it can be erased by temporarily high rates of change. Or multiple OOL events would not necessarily create this pattern.

=====What is the creationists' justification for his prediction of the same thing? =====

Let's say he had some good reason to think god would do it that way. The test is nonetheless metaphysical. Why? Two reasons.

Because it entails a built-in IFF. It entails the premise that "If and Only IF" creation, then the pattern would be observed. Science cannot support IFF's, they require metaphysics for their justification. Science cannot know all truth like religion claims to know.

Going further with this metaphysics, note that creation in this case stakes out a wide berth for itself. By comparing to a random distribution, you end up with any type of signal proving evolution. The Penny paper is a good example of this. The different trees were nowhere close to being congruent, but there definitely was a non random signal present.

So not only is the creationist using an IFF, but it is an incredibly vague test. Any significant variation from completely random gets chalked up as proof of creationism. It may not fit the model very well, but it isn't random.

Cornelius,"False, evolution does not predict that pattern to be observed, for it can be erased by temporarily high rates of change. Or multiple OOL events would not necessarily create this pattern"

THis is astounding. A nested hierarchy is one of the fundamental predictions of common descent. You have now made these statements to the contrary several times now with no justification whatsoever. Your reference for the first statement was the Penny article that makes no reference to high rates of change. And you said you didn't have any reference for the hypothesis of multiple origins of life. so is it safe to say that you are just making these things up as arguments of pretend evolutionists? I do agree, though, that multiple origins of life would not create a nested hierarchy.

"Because it entails a built-in IFF. It entails the premise that "If and Only IF" creation, then the pattern would be observed. "

Again, the researcher is making a statistical test of a hypothesis within a theory. if the null is rejected, the hypothesis is supported. if there is an IFF within this methodology, then it applies to all uses of frequentist statistics including clinical trials, etc.

"The different trees were nowhere close to being congruent, but there definitely was a non random signal present"

Yes, there was a non-random similarity of trees to one another. Just like there is a non-random association between taking a pill and getting over an illness in a clinical trial. again, are you saying that all statistics are metaphysical?

I think the confusion is due to the fact that evolution could have produced a nested hierarchy, without that being evident. People above said that when species split, then it is a nested hierarchy. So saying evolution creates a nested hierarchy is a tautology. But did evolution have to produce a nested hierarchy that is evident today. That is the question. If not, then saying that evolution predicts the evidence we see today is not true.

My apologies for the inappropriate profanity in that post, Cornelius. (For anyone who's curious, I mentioned a recent song which I felt was relevant. However, my posting some of its explicit (though asterisk-censored) lyrics was a little distasteful.)

Now, onto the mind-grappling!

"God wouldn't have done it that way." Huh.

What's so special about biology here? Is biology really any more secular than other sciences? Do IDists find meteorology to be comparatively open to supernatural explanations? Or is the nature of weather such that natural forces are sufficient? (Ha! Tell me what exactly causes lightning. There are plenty of puzzles, and naturalism has not answered them all.)

What about epidemiology? Surely, by your standard, when a scientist rejects the common-sense hypothesis that a disease was caused by divine or demonic action, she is in fact saying "God wouldn't do it that way"? On what grounds, in your view, is the scientist allowed to reject a supernatural explanation?

Is there any science — not just scientists or scientific philosophies, but actual, number-crunching science — built with God as the primary premise?

The point of my simulation argument was that something can be possible without being scientifically useful. At the same time, any premise can be made scientifically useful merely by asking the right questions and making some solid positive predictions. If I were so inclined, I might propose the existence of a regular pattern of program-aberrations, for instance. But I shouldn't expect anyone to listen to me until I at least do something like that. Repeatedly arguing "X is aberrant", by itself, gets us nowhere.

That Darwin did, in fact, occasionally argue "God wouldn't do it that way" is entirely irrelevant, because, despite your protestations, that's not the meat of evolutionary theory; it's not even on the table. There is simply no a priori way to go from "There is no God" to "animals are of common descent" or "allele frequencies change at generally predictable rates." The actual examination of the evidence, not mere anti-theistic pondering, is what yielded these conclusions.

The denial of God is not a premise of biology any more than it is for any other science. The two only relate if one insists that God is defined in such a way as to cause conflict with the notion of seeking natural causes in biology. I could define God as necessarily the creator (by supernatural means) of all stars; does this mean that astrophysics, which studies stellar birth in great detail, goes hand in hand with atheism? That the First Law of astrophysics, despite what the scientists might say, is "God would not create stars in such a way"?

natschuster: People above said that when species split, then it is a nested hierarchy. So saying evolution creates a nested hierarchy is a tautology.

We observe the nested hierarchy. We note, as a mathematical truism, that uncrossed descent with modification leads to a nested hierarchy. This forms the basis of the hypothesis. We then look for evidence to support our hypothesis, including intermediate fossils, biogeographic patterns, mechanisms of evolutionary change, including reproductive isolation. We examine the process in detail, and the broad patterns, too. All the evidence fits the hypothesis very well, and there is no evidence or need for teleology.

Cornelius Hunter: The question was whether the nested hierarchy is a falsifiable prediction of evolution. It isn't. And aside from the fact that evolutionists can explain the absence of the pattern, we also have the fact that the pattern itself has been falsified, many times.

Not even Darwin proposed that the nested hierarchy was perfect. He was quite aware of hybridization between related species, convergence due to natural selection, and suggested that life may have evolved from a few common ancestors resulting in more than one tree (though he was fairly certain of one).

====THis is astounding. A nested hierarchy is one of the fundamental predictions of common descent. You have now made these statements to the contrary several times now with no justification whatsoever. Your reference for the first statement was the Penny article that makes no reference to high rates of change.====

Of course it does (see final paragraph).

====And you said you didn't have any reference for the hypothesis of multiple origins of life. so is it safe to say that you are just making these things up as arguments of pretend evolutionists? I do agree, though, that multiple origins of life would not create a nested hierarchy.====

I'm glad you agree with that uncontroversial observation, but then why do you need a reference? The question was whether the nested hierarchy is a falsifiable prediction of evolution. It isn't. And aside from the fact that evolutionists can explain the absence of the pattern, we also have the fact that the pattern itself has been falsified, many times.

Penny discusses this idea as a hypothetical in the context of a discussion about the philosophy of science. he then dismisses it in the next sentence. so yes, he does mention it but it hardly rises to the level of a seriously considered evolutionary hypothesis.

regarding multiple OOL events: "I'm glad you agree with this uncontroverisal observation, so why do you need a reference?"

because you are once again raising it a serious evolutionary hypothesis, which it is not. I would still like to see a reference. i actually raised that point as a cheeky way to point out that separate creation (or separate origins of life) would not result in a nested hierarchy, another uncontroversial statement with which i'm you'll agree. and i'm sure you'll also agree that it is not a metaphysical statement.

"But there isn't typically an IFF in the method. With evolution there is"

In any frequentist statistical test, you are only testing one hypothesis againt a null hypothesis. of course there are always unconsidered alternative explanations, but this is why you cautiouly interpret results and perform additional tests. just as david penny does when he writes "this supports the theory (of evolution) but of course does not prove it; scientific theories are falsifiable but not provable"

and yes, the nested hierarchy is falsifiable; if exceptions to the hierarchy were the rule rather than the exception then it would be falsified. hypotheses and models do not work perfectly in all cases. you should know this since the protein models in your own published work are only correct 50-65% of the time (barely better than a coin flip).

===Penny discusses this idea as a hypothetical in the context of a discussion about the philosophy of science. he then dismisses it in the next sentence. so yes, he does mention it but it hardly rises to the level of a seriously considered evolutionary hypothesis.===

No, you read that too fast. Far from dismissing it, he admits it is an issue, and concludes with a tip of the hat to Lakatos. You can falsify the prediction of a nested hierarchy, but you can get to evolution, which resides safely behind Lakatos' protective belt. It is not a prediction that could be an evolution falsifier; the only thing that can be falsified is the prediction itself.

===because you are once again raising it a serious evolutionary hypothesis, which it is not. I would still like to see a reference.===

No, you're going off on tangents. I never raised it as a serious evolutionary hypothesis--my point was that it *could* be used as an evolutionary hypothesis to explain other patterns, thus it is another example of why the nested hierarchy prediction is not an evolution falsifier. To be a falsifier, a prediction needs to be the *only* prediction possible for the theory. The nested hierarchy is not the only possible result for evolution.

I imagine a large part of the assertion that evolution does not predict a nested hierarchy is the common ID definition of "evolution" as "the proposition that life arose in a naturalistic and thoroughly unguided manner." Which indeed does not predict a nested hierarchy, so far as that goes.

Is the roundness of planets a prediction from physics? Well, if physics is defined solely as naturalism, then no. If it is defined solely as "Newtonism", then yes (although Newton certainly doesn't account for every other physics observation).

But what if planets weren't round? What if they were square?

Then the theory would have to be revised into something which would account for the data, but wouldn't account for all possible data (unlike Big-Tent ID or the simulation hypothesis).

Likewise, "evolution" could certainly "accommodate" the complete lack of a nested hierarchy — it would just mean that we know biology works with the involvement of some other mechanism! It would be an incredible mystery to try and solve. (Why do all the other apes use a different set of bases? Why is earthworm and ostrich DNA identical? Well, maybe it's because of utterly-unknowable magic. Or maybe it's because… hey, can you hand me that pencil?).

I know that IDists feel that the mysteries have only ever been "solved" with "just so stories", no matter how rigorously worked out the models are. I really don't know what can be done to make them see otherwise. They're missing out! :(

Cornelius,So you say "too fast for congruence" is a serious evolutionary hypothesis in one post and then say you weren't talking about serious evolutionary hypotheses in the next. sure you *could* posit those hypotheses to explain the absence of a nested hierarchy, but neither one is at all convincing- in fact, multiple OOLs with no nested hierarchy would be the antithesis of evolutionary theory.

here is another example of your lightning fast logical shifts. In one post you say that the nested hierarchy is not a falsifiable prediction and then two posts later you say that, referring to the nested hierarchy ".. the only thing that can be falsified is the prediction itself."

let's bring this back to my original point. as i pointed out above, we have solid theoretical reasons to predict a nested hierarchy if common descent is true. if we examined a universal phylogeny, tested its pattern against a null distribution and found that the null hypothesis was strongly supported, the nested hierarchy would be falsified and common descent would not be supported. if not, the NH hypothesis (and common descent) would be supported. no metaphysics, no IFF. given our current state of knowledge, I strongly suspect the latter to be true.

===Again, the researcher is making a statistical test of a hypothesis within a theory. if the null is rejected, the hypothesis is supported. if there is an IFF within this methodology, then it applies to all uses of frequentist statistics including clinical trials, etc.===

Sorry for not addressing this, but I thought it was obvious. The evolutionary use of the null hypothesis is different, in important ways, than such clinical trial testing. Let's have a look.

Problem #1:

In a clinical trial the control group provides the "noise" level. All of the effects (placebo, person-to-person variations, health improvements without the therapy, etc) are represented in the control group. So when the null hypothesis is calculated, it is *against the results of the control group*. If the trial is done correctly, then a statistically significant deviation from the control group is good evidence that pharma1's therapy had an effect. But in performing the trial, they also risk not being able to reject the null hypothesis, and thus revealing their therapy to be ineffectual. You cannot claim the therapy had an effect if the pill group is not statistically different than the placebo group. If you do so then your test is meaningless, as you win either way.

Evolutionists do not do this. Evolution is not harmed either way, as Penny pointed out (in that peer-reviewed paper). Either way, evolution can explain the result.

Problem #2:

Secondly, imagine that pharma2 and pharma3 have competing therapies. If pharma1's therapy passes the clinical trial successfully, and the null hypothesis is rejected, they cannot claim that *only* their therapy can produce positive results. They cannot make claims about pharma2 and pharma3's therapies. They can only make claims about their own therapy.

Again, evolutionists do not follow this method. If they did, all they could say is that the results show that the null hypothesis (of no phylogenetic signal) can be rejected and our prediction succeeded. A successful prediction is one among many predictions, many of which are false. But evolutionists tout this as very powerful evidence.

Problem #3:

If pharma1's therapy passes the clinical trial successfully, and the null hypothesis is rejected, they must also consider the results. The null hypothesis may be rejected, but what if the pill group didn't do any better (just different). What if they did worse? That needs to be reported. One would hardly tout the trial as successful if that were the case.

Again, evolutionists do not do this. Yes, there is non random phylogenetic signal. But the nested hierarchy is repeatedly falsified, in important ways. By "important," I mean the deviations are above the noise -- they are not explained by evolutionary theory, aside from the usual hand-waving (then a bunch of mutations occurred in just the right place). So yes, the null hypothesis is rejected, but this just raises more questions.

So rather than claiming an evolutionary success if their prediction is fulfilled, they claim success merely if the null hypothesis is rejected. Any phylogenetic signal counts as a win for evolution.

Problem #4:

But Problems #1-3 are not problems for evolutionists. Why? Because they hold that the rejection of the null hypothesis is a rejection of creationism. This goes back to Kant, and runs all through the evolution literature up to today. It is not merely a retort of those creationist rascals. Indeed, Carl von Linne's creationist views never had a problem with the nested hierarchy he thought he observed. You won't find this in the Bible anywhere. The nested hierarchy as a falsification of creationism is a uniquely evolutionary metaphysic.

The nested hierarchy is a falsifiable prediction of evolutionary theory. The only way non-nested hierarchy could be incorporated into evolutionary theory is if there were non-gradual changes, e.g. hopeful monster-fast transmutation. We don't observe hopeful monster-fast transmutation. Therefore, Cornelius here is saying the evolution is unfalsifiable because there *might be an alternate universe where hopeful monsters appear superfast.* Sure, in that parallel universe with superfast hopeful monster transmutation, evolution would be unfalsifiable.

But in our universe, evolution is falsifiable. To be more precise, the parameter (change rate) is observable and not a totally unknown, nor unknowable free parameter. Upper and lower limits on change rate (measured in darwins) can be set by measurements of change in the fossil record.

The standard of a scientific theory is not that it be unfalsifiable in all conceivable universes, just in ours-- not that a theory has no parameters, but that it should have the fewest unmeasurable parameters.

As for Dr. Cornelius' statement that there'd be no nested hierarchy if there were multiple OOL's... That's in a parallel universe. In our universe, we observe a single, universal (nearly) genetic code, a single suite of amino acids, identical immortal genes (cytochrome C) etc.

Note here how evolution still kicks creationism's ass! Creationism does not require one nested hierarchy, or two, or three. It does not require any structure at all. Indeed, Stephen Meyer in "Signature in the Cell" said that polyphyly is a PREDICTION of ID! But if polyphyly is disproven, ID is not falsified, naturally!

Creationism/ID of the form that says "God can do whatever he wants" is unfalsifiable: it accomodates all data sets, thus predicting nothing.

But notice the huge advantage of evolution over creationism and ID: evolution theory has one parameter (change rate) that can be measured. But creationism and ID have an infinite number of free parameters, so many, no one has even tried to COUNT THEM! YOU DON'T EVEN KNOW HOW MANY FREE PARAMETERS YOUR THEORY HAS, much less how you could measure them!

How many free parameters are there in "God can do whatever he wants"? How many? How many? HOW MANY FREE PARAMETERS CORNELIUS? How would you even COUNT them?

===The nested hierarchy is a falsifiable prediction of evolutionary theory. The only way non-nested hierarchy could be incorporated into evolutionary theory is if there were non-gradual changes, e.g. hopeful monster-fast transmutation. We don't observe hopeful monster-fast transmutation. Therefore, Cornelius here is saying the evolution is unfalsifiable because there *might be an alternate universe where hopeful monsters appear superfast.* Sure, in that parallel universe with superfast hopeful monster transmutation, evolution would be unfalsifiable. ===

Richie, not at all, this is actually Darwin's argument against design in nature, design in nature is not the same as creationism.

Have it your way. My point remains.

Thanks to Charles Darwin, we are now suppose to believe that evolution is blind and unintelligent. So it's crucial that we go back to Darwin to try and understand why Darwin believed evolution was blind and non-teleological.

We believe evolution to be blind and non-teleological because there is no evidence for it being anything else. That really is it.

Origin of species are full of these straw god arguments, for example animals migrating to different oceanic islands was actually claimed to be evidence for evolution Darwin argued because his straw god would have created the animals independently on the different islands. All Darwin had to prove was that some animals migrated to oceanic islands.

What utter nonsense.

I'm guessing you haven't read the Origin of Species, because if you have you clearly haven't grasped it in the slightest. The point about migrating animals is one about nested hierarchies - species that have migrated from a mainland onto a set of islands will resemble others on their island more than ones on other islands, but will even resemble those more than their mainland 'ancestor' species. It is a specific pattern which the theory of evolution accounts for. And it is not based on presuppositions of what God what or would not design. Darwin noted patterns of relatedness. Darwin came up with a theory explaining those patterns of relatedness. God doesn't even get a look in. Expect, of course, from bonkers ID-ers who desperately try to make excuses for him and smuggle him in through the back door.

Observed patterns of relatedness are evidence. The theory of evolution explain the evidence - in a way that is testable. Therefore it is science. That's it - the theory of evolution is not based on any metaphysical assumptions (apart from the one about not using the supernatural to explain natural phenomenon, but EVERY scientific theory is based on that - it is simply a prerequisite for doing science).

Oh Darwin believed in God all right, just that he thought God would be in a lot of trouble if God was directly involved in Creation. Darwin felt evolution could get God off the hook, this is why many theologians were excited about his idea while the scientists were less impressed.

Again, total nonsense. I don't mind people not knowing anything about Darwin as a person - it's not like we need to know anything about him to understand his theory. But when you ascribe false motives to him to feed your paranoid conspiracy theories, I take issue.

Funny when evolutionists thought the opposite was some of the most powerful evidence for evolution.

When did anyone ever think the opposite was true?

“Wells repeatedly fails to grasp the evidential value of phenomena [i.e., dissimilarities in early embryos] that can be understood only as the result of a historical process.”

There will be dissimilarities between any two things which are not identical. The issue is that early embryos look very similar and only later develop their differences. No-one ever said they were identical.

I'm a little confused about the embryos. It was my understading that it was the similarities between embryos that was evidence for evolution. The probelm with that is that they are not all that similar. Haeckel confessed to falsifying embryo drawings. Moreover vertebrate embryos only resemble each other during short period in the middle of development. They do not resemble each other during gastrulization. The cells and tissues follow very different developmental pathways. And at the bastula stage, mammal embryos are so different than other vertebrates that they are given a different name, blastocysts. Please enlighten me.

The phase vertibrate embryos pass through where they look very similar is called the phylotipic stage, and they do look remarkably similar indeed (though no, not identical).

At this stage the embryos develop features which will turn into different structures in the adult form, for example, the embryo branchial arches (nicknamed 'gill slits'). These ridges go on to form parts of the jaw, throat and neck in humans, and proper gills in fish.

Think about the implications of this for a moment - the same developmental proto-features are being TURNED INTO different features. Evolution provides an explanation for this. ID and other forms of Creationism do not, other than the catch-all explanation of 'God wants it that way - you can't prove otherwise'.

However, whenever you hear Creationists mention this, they will inevitable dredge up poor old Ernst Haeckel - a late-nineteenth century biologist. He observed that vertibrate embroys were very similar. The theory of evolution being a fledgeling idea, he came up with a hypothesis - perhaps all embroys relive their evolutionary history in the egg/womb, as in, a mammal embryo become a full fish, then amphibian, then reptile, then finally mammal before birth.

This hypothesis turned out to be false, and the drawings he did to support his case did exaggerate the similarity.

However, this does not discredit the observations themselves. Vertibrate embryos really do pass through a stage where they are extremely similar, and develop features which will turn into a variety of differing features and organs in the adult form. And evolution still provides an explanation, even if Ernst Haeckel did not.

===Penny discusses this idea as a hypothetical in the context of a discussion about the philosophy of science. he then dismisses it in the next sentence. so yes, he does mention it but it hardly rises to the level of a seriously considered evolutionary hypothesis.===

And then commented:

No, you read that too fast. Far from dismissing it, he admits it is an issue, and concludes with a tip of the hat to Lakatos. You can falsify the prediction of a nested hierarchy, but you can get to evolution, which resides safely behind Lakatos' protective belt. It is not a prediction that could be an evolution falsifier; the only thing that can be falsified is the prediction itself.

Either way, I don’t see that Penny is saying what Hunter claims he is saying. Here is my transcription of the last paragraph of Penny et al:

An interesting philosophical question would arise if the results of this work had falsified the prediction that the trees would be similar. Would this disprove the theory of evolution, or could it just mean that the sequences had changed so rapidly that they had lost all information about their early history, thus contradicting the hypothesis of Zuckerkandl and Pauling? It could be argued that because proteins from different species can be aligned so readily, this in itself is independent evidence that the proteins retain evolutionary information. However, it is probably true that specific predictions from hypotheses, rather than the hypotheses themselves, are falsifiable. This idea is inherent in Popper’s writing, but is more clearly expressed by Lakatos. To this extent, we suggest that Popper’s criticisms of evolutionary theory have shown incompleteness in the application of evolutionary theory, but at the same time evolutionary theory has helped clarify some inadequacies in Popper’s model of the growth of knowledge.

I submit that this issue, whatever interest it may hold for philosophers, is moot scientifically, because the evidence supports descent with modification, which is the key claim of evolutionary theory.

Suppose you tossed an apple and it fell up. Would that "falsify gravitation"? No, because(a) there is an enormous amount of independent evidence for an attractive force between masses, and(b) you have made just one observation, which may be(1) a flawed mismeasure/optical illusion,(2) indicative of some other known force at work, such as magnetism or buoyancy, or(3) indicitave of some unknown force at work.

In fact, it has to be one of those three. At no point do we say, "Well, I guess it turns out there never was an attractive force between masses after all!" Even if, starting tomorrow, gravitation suddenly stopped working on fruit and only fruit, we would still be justified in the assertion that gravitation had been at work before, and remains< at work except, strangely, for fruit — for reasons we would be very anxious to work on and not just chalk up to "unknown intelligent agency".

In a sense, the generic notion of gravitation is "beyond" falsification, because it has been so widely observed. Sub-theories ("gravity will cause X") and super-theories ("gravitation is caused by Y") are still subject to falsification. I would say the same is true of evolution and the nested hierarchy. That populations change over time as a result of allele change is indisputable, and that this has resulted in a tree of life is indisputable. The explanations for these phenomena, and the predictions based on them, are still subject to debate.

You are referring to only a small subset of clinical trials, probably the least frequently performed kind. double blind, placebo controlled studies are ideal but are difficult and expensive to run and are not performed as often as observational studies or cohort studies. yet people make life-and-death decisions based on these studies. are you saying that all of these studies are metaphysically based and are not valid science? now let's take a look at your own work. In your paper (Proteins 2003 50:572-579) you build a model to predict centroids of proteins from amino acid sequences. you don't actually use any statistics here, but instead rely on the old "eyeball the data" approach. you claim that predicted results are accurate (in other words, your model works better than a random model, sounds familiar), but don't use a negative control. so in your strict view of science, these results are meaningless. then you do quite a bit of hand waving to explain away some discrepancies in your results, blaming the lack of fit on low sample size. this paper was published 7 years ago, so perhaps you've grown more rigid in your definition of science. are you going to retract this paper anytime soon?

====You are referring to only a small subset of clinical trials, probably the least frequently performed kind. double blind, placebo controlled studies are ideal but are difficult and expensive to run and are not performed as often as observational studies or cohort studies. yet people make life-and-death decisions based on these studies. are you saying that all of these studies are metaphysically based and are not valid science?===

You'll have to elaborate on why you think an observational or cohort study is no different than the evolutionary claim about the nested hierarchy. It is not at all clear why you see this parity, and why you see the evolution's metaphysics as no different than such studies. I could try to explain, but I might not address what you are thinking of. I tried that once and it didn't work. So I think you need to give a specific example, or otherwise elaborate on why you see the parity.

Cornelius,"You'll have to elaborate on why you think an observational or cohort study is no different than the evolutionary claim about the nested hierarchy"

Because the statistical test employed is the same and the results are interpreted in the same way. In an observational study, there is no control group and effects of e.g. obesity are correlated with e.g. heart disease. the hypothesis is that obesity causes heart disease, and the prediction is that obesity and heart disease will be positively correlated. they found this statistically significant positive correlation, i.e. the null hypothesis of no relationship was rejected. the alternative hypothesis, in the predicted direction, was supported, suggesting that overweight women are more likely to get heart disease.similarly, we propose the hypothesis of common descent and the prediction that patterns of descent will form Markov-chain like nested hierarchies. We find that they form such nested hierarchies (not just any old pattern), rejecting the null hypothesis of no pattern. the alternative hypothesis of common descent, with the specifically predicted pattern of nested hierarchies, was supported, suggesting that organisms living today descended with modification from ancestral forms.you use this same methodology (although without actually using those troublesome statistics) in your own work on proteins. so what's the problem again?

I understand that Haeckle not only faked the drawings but was very selective in his choice of samples. Some closely related species have embryos that don't look all that much alike. And if similarities in one stage imply common descent, then the very great differences at earlier stages that I mentioned above should imply the opposite.

Embryos have have many more points of similarity during the phylotypic stage than in their developed forms. That's simply a fact. The gastrula stage varies due to the structure and environment of the egg, such as the size of the yolk.

And whatever the reason, the during the gastrula stage the cells and tissues from the embryos from the different vertebrate orders follow very different paths. And birds and reptiles can have similar sized eggs. And saying they have different egg environments and structures only pushes the problem back one step. And I would expect things that are similar in the end product to resemble each other during the manufacturing process. I imagine a car and a truck would look the same at some point on the assembly line.

David said... Was it Quine who pointed out that for any apparent falsification of an hypothesis about a collection of empirical data, it is always possible to save the hypothesis with sufficient ad hoc assumptions?

A great illustration of that phenomenon is Sagan's Dragon. It's also often considered to relate to the Ptolemaic epicycles. (Interestingly, historical evidence for the popular notion that astronomers kept adding epicycles to continually justify geocentrism seems scant; but that's irrelevant to what I'm going to say here.)

As I see it, whenever evaluating if spurious ad hoc reasoning is at work, one must consider the alternate hypotheses. In the case of Sagan's Dragon, the alternate hypothesis is simple and obvious: the null hypothesis that there is no dragon. No anomalies exist which require anything like a dragon to explain them, so no further hypothesis is necessary.

In the case of Ptolemaic astronomy, the alternate hypothesis is rather trickier: that something else (the Sun) serves as the center point of the objects' arcs of motion. In order to refute the epicycles — even though we now "know" epicycles are unnecessary — you need to have an alternative. It's not enough to say "epicycles are just ad hoc", or (worse still, in hindsight) "natural/undirected forces are clearly inadequate to account for the observed astronomical facts".

Right now, I can think of at least one area of science with a major "ad hoc" premise holding things together — dark matter. Instead of assuming and testing its existence/nonexistence, we could just say, "clearly, all our prior assumptions about the fundamental laws are very incorrect." But by itself, this gets us nowhere.

It all comes down to the same darn question asked in this post's title. If you think you're seeing epicycles… what's your heliocentrism? And how is it to be distinguished from the "hypothesis" (indescribable supernatural design) which we all know is unnecessary when dealing with matters of astronomy, meteorology, or any other non-biological science?

===Because the statistical test employed is the same and the results are interpreted in the same way. In an observational study, there is no control group and effects of e.g. obesity are correlated with e.g. heart disease. the hypothesis is that obesity causes heart disease, and the prediction is that obesity and heart disease will be positively correlated. they found this statistically significant positive correlation, i.e. the null hypothesis of no relationship was rejected. the alternative hypothesis, in the predicted direction, was supported, suggesting that overweight women are more likely to get heart disease.===

Why did you conclude "suggesting that overweight women are more likely to get heart disease" rather than "suggesting that obesity causes heart disease"? Do you implicitly include the hypothesis, or is there a reason you didn't mention it?

natschuster: Are you sure your not being selective about the embryos you selected?

They're selected to represent diverse organisms so that it is easy to verify that they have many more points of similarity during the phylotypic stage than in their developed forms. Ask if you are curious.

natschuster: And whatever the reason, the during the gastrula stage the cells and tissues from the embryos from the different vertebrate orders follow very different paths.

Not for "whatever the reason," but because they have been adapted to their particular developmental pattern, in particular, the presence of a yolk. Yolks are the derived trait. Interestingly, humans develop an umbilical vesicle, homologous to the yolk sac, while the genes for yolk are non-functional pseudogenes.

Arendt & Nübler-Jung, Rearranging gastrulation in the name of yolk: evolution of gastrulation in yolk-rich amniote eggs, Mechanisms of Development 1999.

Cornelius,just a typo, i meant the hypothesis that obesity causes heart disease was supported. and if you're going to go down the "correlation does not equal causation" route- thanks, i already know that. i hope you will also address the example of your own published work that uses the same methodology of comparing a predicted to a measured pattern.

" if you're going to go down the "correlation does not equal causation" route- thanks, i already know that. "

Which raises the question of how you possibly could think the evolutionary argument that the nested hierarchy proves evolution is no different than your observational study example of obesity and heart disease being correlated. The most we can conclude is:

1. Obesity and heart disease are correlated.2. The hypothesis that obesity *causes* heart disease is not falsified.3. The correlation supports the hypothesis that obesity causes heart disease because it is a fulfilled prediction.

The case of the nested hierarchy is different, as I pointed out. You made the distinction between a double blind study and an observational study, but an observational study is still not like the evolutionary claim. Here's why:

Problem #1:

In an observational study the prediction is binding. If the hypothesis is that obesity that we can observe causes heart disease that we can observe, then there better be a correlation between these two observations. In performing the study, they risk not being able to reject the null hypothesis, and thus falsifying the hypothesis. If you cannot falsify the hypothesis then your test, insofar as a test of the hypothesis, is meaningless.

Evolutionists do not do this. Evolution is not harmed either way, as Penny pointed out (in that peer-reviewed paper). Either way, evolution can explain the result.

Problem #2:

Secondly, imagine that observed correlation is not a causation. That is a possibility, which is why rejection of the null hypothesis does not prove the hypothesis that there is correlation, it merely supports the hypothesis. That's a much weaker conclusion (it doesn't falsify the hypothesis).

Again, evolutionists do not follow this method. If they did, all they could say is that the results show that the null hypothesis (of no phylogenetic signal) can be rejected and our prediction succeeded. A successful prediction is one among many predictions, many of which are false. But evolutionists tout this as proof of evolution, not merely as a successful prediction.

Problem #3:

You can have a rejection of the null hypothesis that does not support the hypothesis, and indeed falsifies it. Namely, in this example of obesity and heart disease, you could have a negative correlation. That is non random, but falsifies the hypothesis that obesity causes heart disease. The results show just the opposite.

Again, evolutionists do not do this. Yes, there is non random phylogenetic signal. But the nested hierarchy is repeatedly falsified, in important ways. By "important," I mean the deviations are above the noise -- they are not explained by evolutionary theory, aside from the usual hand-waving (then a bunch of mutations occurred in just the right place). So yes, the null hypothesis is rejected, but this just raises more questions.

So rather than claiming an evolutionary success if their prediction is fulfilled, they claim success merely if the null hypothesis is rejected. Any phylogenetic signal counts as a win for evolution.

Problem #4:

But Problems #1-3 are not problems for evolutionists. Why? Because they hold that the rejection of the null hypothesis is a rejection of creationism. This goes back to Kant, and runs all through the evolution literature up to today. It is not merely a retort of those creationist rascals. Indeed, Carl von Linne's creationist views never had a problem with the nested hierarchy he thought he observed. You won't find this in the Bible anywhere. The nested hierarchy as a falsification of creationism is a uniquely evolutionary metaphysic.

--------using a random distribution (i.e. not a nested hierarchy) as a null model is a standard in all hypothesis-based statistical tests. or else you would say that the results of all statistical tests are religious, e.g.

"God wouldn't make the results of this drug trial different than random at the level of p<0.05 , so the drug must be the cause of these people getting better."--------

No, not at all. You're confused on this. The only way the evolutionists methods could qualify as science, and be comparable to the observational studies and clinical trials, would be if they said: we have this hypothesis, we're going to collect data, and if the data matches what the hypothesis predicts (statistically) then all we will claim is that the study *supports* the hypothesis. And if the data do not match, then we'll drop the whole idea.

Conversely, the way that the observational studies would have to be done to be comparable to evolution would be like this. Health researchers would say that after years of study, they conclude that an unknown bacteria causes heart disease and there can be no other cause. Now the key question is, is there or is there not heart disease. A massive study is undertaken, and the conclusion is there is no question about it, there is heart disease. Therefore, it is a fact that this unknown bacteria exists, and is doing just what we thought it did.

Also, it is often hypothesized that this bacteria acts rapidly. For example, when expected patterns are not observed, the researchers say that the patterns was erased by rapid, high levels, of the bacteria activity. The heart disease was there, but then the additional actions of the bacteria causes other effects, and the heart disease went away.

Cornelius,"Which raises the question of how you possibly could think the evolutionary argument that the nested hierarchy proves evolution"

where did i say the nested hierarchy proves evolution? where did anyone say that?

problem #1: you are still confused about hypotheses v theories. yes, evolutionary hypotheses have been falsified. does this merit falsification of the entire theory? let's say that there was no correlation between obesity and heart disease. would this falsify the entire theory of exercise physiology?

problem #2: again, if anyone is saying the nested hierarchy is proof of evolution, they are wrong. you should be able to see why from my previous comments.

Problem #3: I pointed out that the specific prediction of a nested hierarchy was met, not just any phylogenetic signal. similarly, in the Penny paper, the specific prediction of congruence between trees was met. the trees could have been even more incongruent that random, and I'm afraid, contrary to your statement, that he would not label such a pattern as a succesful prediction just because it was different than random. Problem # 4: see problem #3- we are making specific predictions about patterns, not just any pattern. so we are not just rjecting the null hypothesis in any old direction. you really do seem to think that all statistics are metaphysical. no wonder you didn't use them in your own work.

Cornelius,"we have this hypothesis, we're going to collect data, and if the data matches what the hypothesis predicts (statistically) then all we will claim is that the study *supports* the hypothesis. And if the data do not match, then we'll drop the whole idea"this is exactly what happens in evo bio journals all the time. I don't recall ever reading a paper that said "our hypothesis is supported, therefore the theory of evolution is proven", or "our hypothesis was not supported, therefore the theory of evolution is false."

"where did i say the nested hierarchy proves evolution? where did anyone say that?"

"The several subordinate groups in any class cannot be ranked in a single file, but seem clustered round points, and these round other points, and so on in almost endless cycles. If species had been independently created, no explanation would have been possible of this kind of classification." --Darwin

"Could the single artisan, who has no one but himself from whom to steal designs, possibly be the explanation for why the Creator fashioned life in a hierarchical fashion—why, for example, reptiles, amphibians, mammals, and birds all share the same limb structure?"--N. Eldredge

"Problem #3: I pointed out that the specific prediction of a nested hierarchy was met, not just any phylogenetic signal. similarly, in the Penny paper, the specific prediction of congruence between trees was met. the trees could have been even more incongruent that random,"

No, there are all kinds of phylogenetic incongruences which no one takes as contra indicative of evolution even though there is no plausible evolutionary explanation (even in the Penny paper the "similar" trees have significant differences).

And the article you sited explains who reptiles and bords have different gastruzation than amphibians. But amphibians have different gastruzation than fish, with similar eggs, and birds and reptiles have different gastruzation, even though they have similar eggs.

natschuster: And the article you sited explains who reptiles and bords have different gastruzation than amphibians. But amphibians have different gastruzation than fish, with similar eggs, and birds and reptiles have different gastruzation, even though they have similar eggs.

Not as different as they might appear at first glance, and the article provides an evolutionary framework for understanding the differences.

natschuster: My point is that maybe there are different embryos that don't look that much alike.

Nothing is stopping you from studying the topic, but you don't even seem curious about the examples already provided.

Cornelius,re: your quotations. I was looking more for something from the peer-reviewed scientific literature. as I said, I do not agree that the nested hierarchy proves evolution. It does, however, support the hypothesis of common descent.

"even in the Penny paper the "similar" trees have significant differences)"

this is why we do statistics. in a correlation of obesity and heart disease there are bound to be cases that don't fit, but the overall predicted pattern can still be there. the same thing goes for your protein model- many predicted and expected values didn't fit, but the overall pattern was (weakly) there (as far as i can tell just eyeballing it). are you really bashing your own minimal contributions to science here?

========= re: your quotations. I was looking more for something from the peer-reviewed scientific literature. =========

So evolutionists claim evolution is a scientific fact, and when you criticize the claim they respond: "that's not from the peer-reviewed literature..." Sorry, but the peer-reviewed literature does not typically engage in proposing, defending and mandating asinine theories.

=========As I said, I do not agree that the nested hierarchy proves evolution. It does, however, support the hypothesis of common descent.=========

Of course, but that's not the claim. There's all kinds of evidence that falsified predictions of evolution and common descent. If you're actually interested in objectively evaluating the theory then you'd need to engage those evidences and how they bear. You certainly would not come to the conclusion that evolution is a scientific fact.

========= "even in the Penny paper the "similar" trees have significant differences)"

this is why we do statistics.=========

No, this is why we do science. Science is more than running piles of data through the computer's statistics package.

======= in a correlation of obesity and heart disease there are bound to be cases that don't fit, but the overall predicted pattern can still be there.=======

No, the question is not "Did I pass some statistical test of randomness which knows nothing of the science at hand," rather, the question is "Are the outliers plausibly explained by my theory?" That, however, would raise serious problems for evolution, so instead the tout their passing of randomness tests, because such results falsifies "independent origin." That's what the Penny paper is all about. They could care less about trying to explain the wide incongruencies, their conclusion was the there was signal, and so "indendendent origin" was disproven. It's all metaphysical.

I could make the flat earth theory or geocentrism look like facts if passing statistical tests was all that counted. That's why we have scientists, and not statisticians, doing science. Phylogenetic outliers are *not* plausibly explainable by evolution, but that doesn't matter to evolutionists.

Cornelius,"So evolutionists claim evolution is a scientific fact"I don't know why you keep attributing views to me that i don't hold. where did i ever say evolution is a scientific fact? it is a fact that evolution occurs, but the theory of evolution can never be a fact just by definition.

"Sorry, but the peer-reviewed literature does not typically engage in proposing, defending and mandating asinine theories."

there are over 30 peer-reviewed scientific journals devoted exclusively to evolutionary biology, and many more that feature evolution as a focus. yet now by your own admission the statement that the nested hierarchy proves evolution has never appeared in any of this literature. yet you continue to claim that this statement is accepted by all evolutionary biologists. why is that?

me: "it does, however, support the hypothesis of common descent"

you: "Of course, but that's not the claim"

me: it is the claim i just made. i'm glad you agree with me.

"You certainly would not come to the conclusion that evolution is a scientific fact"

see above

the rest is all about your irrational loathing of statistics. of course the statistics don't know anything about the science at hand, they are just an objective tool used by the scientist who does know the science. outliers are certainly interesting but are taken into account by the stats. if there are enough of them, they will affect the broad pattern, if not, you can take note of them and investigate later. otherwise, you might conclude that, because two of your samples were incredibly obese but have the hearts of olympic marathoners, there is no relationship between obesity and heart health, even though the expected relationship is seen in the 200 other samples.

as for proving flat earth with stats, i would like to see that as well. let's start by statistically examining the flat earth hypothesis that you will fall off the end of the earth if you sail too far. in that case, the null hypothesis is supported at the 1.00 level. not too promising so far.

I don't know why you keep attributing views to me that i don't hold. where did i ever say evolution is a scientific fact? it is a fact that evolution occurs, but the theory of evolution can never be a fact just by definition.======

Classic. What, me say evolution is a fact? Nooo, I just said it is a fact that evolution happens. Right.

Cornelius,when i say evolution occurs, i am referring to eg antibiotic resistance, which you agree constitutes an example of evolution. that evolution occurs, as is illustrated by these examples, is a fact.